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Recent Releases of https://github.com/brsynth/rptools

https://github.com/brsynth/rptools - Release 6.5.0

6.5.0 (2023-11-29)

⚠ BREAKING CHANGES

  • args: change arg name withorphanspecies

Features

  • rplibs>rpSBML: add rmisolatedspecies() (66895b1)

Bug Fixes

  • rplibs: store group.getId() before removing (8263282)

Tests

  • rpfba: fit to new arg (7483010)
  • rplibs: add test to new rpSBML method (02a92e4)

chore

  • args: change arg name withorphanspecies (b56cb0f)

Build Systems

  • environment.yaml: python until 3.10 (7739b41)
  • tag: put back jobs (784e0ed)

- HTML
Published by github-actions[bot] over 2 years ago

https://github.com/brsynth/rptools - Release 6.4.1

6.4.1 (2023-11-21)

Bug Fixes

  • rpfba: fit type for 'merge' option in tests (c535ebf)

Build Systems

  • environment.yaml: fix pkg ver (aedc9af)

- HTML
Published by github-actions[bot] over 2 years ago

https://github.com/brsynth/rptools - Release 6.4.0

6.4.0 (2023-11-20)

Features

  • rpfba: add outfile name of rpfba merged model (cbf7e86)

- HTML
Published by github-actions[bot] over 2 years ago

https://github.com/brsynth/rptools - Release 6.3.3

6.3.3 (2023-11-20)

Bug Fixes

  • rpPathway: EC numbers list (2ea5ab8)
  • rpPathwy: invert test Compound (89453a1)

Tests

  • rplibs: change input dataset name attr (e9a442b)
  • rplibs: rm import (acc2f1a)

- HTML
Published by github-actions[bot] over 2 years ago

https://github.com/brsynth/rptools - Release 6.3.2

6.3.2 (2023-10-25)

Bug Fixes

Build Systems

  • environment: cobra >=0.26.3 (6066d0d)
  • environment.yaml: rm pkgs (e902540)
  • environment.yaml: update (e6f0f23)
  • environment.yaml: update (1043fef)

- HTML
Published by github-actions[bot] over 2 years ago

https://github.com/brsynth/rptools - Release 6.3.1

6.3.1 (2023-10-23)

Bug Fixes

  • fit to new rpPathway specs (d69377d)

- HTML
Published by github-actions[bot] over 2 years ago

https://github.com/brsynth/rptools - Release 6.3.0

6.3.0 (2023-10-20)

⚠ BREAKING CHANGES

  • rpextractsink: genSink return a dict
  • rpextractsink: stop converting spe id

Features

  • rpextractsink: add standalone mode (7fd5f8b)

Bug Fixes

  • rpextractsink: args typo (880cf87)
  • rpfba: remove medium feature (0bd7bc3)
  • rpfba: test (7476c2f)
  • rplibs: fit to MIRIAM as list (972e2db)
  • rplibs: fix MIRIAM cross-ref reading (070d05b)

Build Systems

Tests

  • rpextractsink: clean up (76fd865)
  • rpextractsink: reduce code (2a75589)
  • rpextractsink: split tests + test wrong comp (76c98e7)
  • rpscore: add tests (ee18a0e)

chore

  • rpextractsink: genSink return a dict (08feb51)
  • rpextractsink: stop converting spe id (3dc2012)

Styles

- HTML
Published by github-actions[bot] over 2 years ago

https://github.com/brsynth/rptools - Release 6.2.3

6.2.3 (2023-03-17)

- HTML
Published by github-actions[bot] over 3 years ago

https://github.com/brsynth/rptools - Release 6.2.2

6.2.2 (2023-02-15)

Bug Fixes

  • rpextractsink: [WIP] detect more dead end metabolites (fa84570)
  • rpextractsink.py: refine removal of dead end metabolites (e7e08a4)

Tests

- HTML
Published by github-actions[bot] over 3 years ago

https://github.com/brsynth/rptools - Release 6.2.1

6.2.1 (2023-02-09)

Bug Fixes

  • rplibs: put back 'rp_' prefix for model ID (aa5af8c)

Tests

  • rpcompletion: fit to 'rp_' (f5a685a)

- HTML
Published by github-actions[bot] over 3 years ago

https://github.com/brsynth/rptools - Release 6.2.0

6.2.0 (2023-01-30)

Features

- HTML
Published by github-actions[bot] over 3 years ago

https://github.com/brsynth/rptools - Release 6.1.0

6.1.0 (2023-01-10)

Features

  • rpfba: if --merge, output merged file (cadd5c6)

- HTML
Published by github-actions[bot] over 3 years ago

https://github.com/brsynth/rptools - Release 6.0.2

6.0.2 (2023-01-04)

Build Systems

  • environment.yaml: pin numpy version (25a681f)

Continuous Integration

  • github: update action version (970ab9e)

- HTML
Published by github-actions[bot] over 3 years ago

https://github.com/brsynth/rptools - Release 6.0.1

6.0.1 (2022-11-17)

Bug Fixes

  • rplibs: sort lists to compare (8b46001)
  • rpThermo: remove choices for ionic_strength (a8ab603)

Tests

  • rpcompletion: check if all ref files are generated (1d18993)
  • rplibs: add test for rpReaction.eq (1ab8d40)

- HTML
Published by github-actions[bot] over 3 years ago

https://github.com/brsynth/rptools - Release 6.0.0

6.0.0 (2022-11-16)

⚠ BREAKING CHANGES

  • rprank: switch pathway names into pathway filenames

Features

Bug Fixes

  • Args.py: correctly print default compartment (d8ef826)
  • rpthermo: accept floating values for pH (7fac69c)

Continuous Integration

  • github: restore all tests (8a654d3)
  • github: restore tests for all platforms (557cdfc)

Tests

  • rpcompletion: test if OK (995d699)
  • rpCompletion: add assert (9546057)

Build Systems

  • github: change miniconda version (f026927)

chore

  • rprank: rename pathways (5cd31b9)

- HTML
Published by github-actions[bot] over 3 years ago

https://github.com/brsynth/rptools - Release 5.13.1

5.13.1 (2022-06-23)

Tests

  • rpSBML: fit assert according to previous changes (ed51b6f)

Styles

  • rpSBML: polish comments (17ade84)

Build Systems

  • environment: put back equilibrator-api (c5a898a)

- HTML
Published by github-actions[bot] almost 4 years ago

https://github.com/brsynth/rptools - Release 5.13.0

5.13.0 (2022-06-21)

Features

  • rpExtractSink: add --cache-dir option (9feed24)

Build Systems

- HTML
Published by github-actions[bot] almost 4 years ago

https://github.com/brsynth/rptools - Release 5.12.3

5.12.3 (2022-04-17)

- HTML
Published by github-actions[bot] about 4 years ago

https://github.com/brsynth/rptools - Release 5.12.2

5.12.2 (2022-04-14)

Bug Fixes

  • environment: add new dependency for pandas requirements (39cbeae)
  • rpSBML: well-format species sid (libSBML) (51bf67f)

- HTML
Published by github-actions[bot] about 4 years ago

https://github.com/brsynth/rptools - Release 5.12.1

5.12.1 (2022-01-28)

Build Systems

  • github: temp rm windows tests (3cee2c9)

- HTML
Published by github-actions[bot] over 4 years ago

https://github.com/brsynth/rptools - Release 5.12.0

5.12.0 (2022-01-17)

Features

  • rplibs: rpSBML, add from_cobra() (cbf8920)
  • rplibs: rpSBML, add has_reaction() (0d54572)
  • rplibs: rpSBML, add has_specie() (0f9be21)
  • rplibs: rpSBML, add to_cobra() (07ede79)

Bug Fixes

  • github: ruby version (159e582)
  • MANIFEST.IN: add fba medium folder (4975c2a)
  • rpfba: check compartment (49e62be)
  • tests/rpextractsink: specify compartment (af486f1)

Continuous Integration

  • github: remove ruby version (5a972b5)

Tests

  • rplibs: rpSMBL, search_* functions (5df574b)

- HTML
Published by github-actions[bot] over 4 years ago

https://github.com/brsynth/rptools - Release 5.11.1

5.11.1 (2021-12-16)

- HTML
Published by github-actions[bot] over 4 years ago

https://github.com/brsynth/rptools - Release 5.11.0

5.11.0 (2021-12-09)

Features

  • rplibs: add runnable 'stats' command (9483c58)

- HTML
Published by github-actions[bot] over 4 years ago

https://github.com/brsynth/rptools - Release 5.10.0

5.10.0 (2021-12-07)

Features

  • rprank: add rpRank module (e24043b)

- HTML
Published by github-actions[bot] over 4 years ago

https://github.com/brsynth/rptools - Release 5.9.2

5.9.2 (2021-11-10)

Bug Fixes

  • rptools: handle temp file on windows (c82bf5b)

Build Systems

- HTML
Published by github-actions[bot] over 4 years ago

https://github.com/brsynth/rptools - Release 5.9.1

5.9.1 (2021-11-08)

Bug Fixes

Build Systems

  • setup: add utf-8 coding (c095732)

- HTML
Published by github-actions[bot] over 4 years ago

https://github.com/brsynth/rptools - Release 5.9.0

5.9.0 (2021-11-08)

Features

  • rpfba: add buildminimalmedium() in medium (c37962e)
  • rpfba: add minimal_medium feature (9a4dd89)

Build Systems

Documentation

Tests

  • rpfba: add test for buildminimalmedium() (bfdb2d6)
  • rplibs: rpfba, runFBA(), checkSBMLcompartment(), checkSBMLrxnid() (8563a15)

- HTML
Published by github-actions[bot] over 4 years ago